Jointly Accurate Sv Merging with Intersample Network Edges
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcfs{:bash}
:list
The VCF files that need to be merged
*.{vcf,vcf.gz}
bams{:bash}
Optional - The BAM files from which the VCFs were created
*.bam
bais{:bash}
Optional - The BAM index files from which the VCFs were created
*.bai
sample_dists{:bash}
:file
Optional - A txt file containing the distance thresholds for each sample
*.txt
meta2{:bash}
Groovy Map containing fasta information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
Optional - The reference FASTA file used to create the VCFs
*.{fasta,fa}
meta3{:bash}
Groovy Map containing fasta index information e.g. [ id:‘test’, single_end:false ]
fasta_fai{:bash}
Optional - The index of the reference FASTA file used to create the VCFs
*.fai
chr_norm{:bash}
Optional - A txt file containing the chromosomes and their aliases for normalization
vcf{:bash}
*.vcf.gz{:bash}
The merged VCF file
*.vcf.gz
versions_jasminesv{:bash}
${task.process}{:bash}
:string
The name of the process
jasminesv{:bash}
The name of the tool
jasmine 2>&1 | grep "version" | sed "s/Jasmine version //"{:bash}
:eval
The version of the tool
versions_bgzip{:bash}
bgzip{:bash}
bgzip --version | head -1 | sed -e "s/bgzip (htslib) //"{:bash}
The expression to obtain the version of the tool
versions{:bash}
Software for merging structural variants between individuals
